{"id":"https://openalex.org/W4313702127","doi":"https://doi.org/10.1093/bioinformatics/btac667","title":"Metadata retrieval from sequence databases with <i>ffq</i>","display_name":"Metadata retrieval from sequence databases with <i>ffq</i>","publication_year":2022,"publication_date":"2022-10-07","ids":{"openalex":"https://openalex.org/W4313702127","doi":"https://doi.org/10.1093/bioinformatics/btac667","pmid":"https://pubmed.ncbi.nlm.nih.gov/36610997"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac667","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac667","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac667/48942763/btac667.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac667/48942763/btac667.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5028322479","display_name":"\u00c1ngel G\u00e1lvez-Merch\u00e1n","orcid":"https://orcid.org/0000-0001-7420-8697"},"institutions":[{"id":"https://openalex.org/I122411786","display_name":"California Institute of Technology","ror":"https://ror.org/05dxps055","country_code":"US","type":"education","lineage":["https://openalex.org/I122411786"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"\u00c1ngel G\u00e1lvez-Merch\u00e1n","raw_affiliation_strings":["Division of Biology and Biological Engineering, California Institute of Technology , Pasadena, CA 91125, USA"],"affiliations":[{"raw_affiliation_string":"Division of Biology and Biological Engineering, California Institute of Technology , Pasadena, CA 91125, USA","institution_ids":["https://openalex.org/I122411786"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085427795","display_name":"Kyung Hoi Min","orcid":"https://orcid.org/0000-0003-0894-4017"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kyung Hoi (Joseph) Min","raw_affiliation_strings":["Department of Computer Science and Electrical Engineering, Massachusetts Institute of Technology , Cambridge, MA 91125, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Electrical Engineering, Massachusetts Institute of Technology , Cambridge, MA 91125, USA","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020008219","display_name":"Lior Pachter","orcid":"https://orcid.org/0000-0002-9164-6231"},"institutions":[{"id":"https://openalex.org/I122411786","display_name":"California Institute of Technology","ror":"https://ror.org/05dxps055","country_code":"US","type":"education","lineage":["https://openalex.org/I122411786"]},{"id":"https://openalex.org/I4210090226","display_name":"Mathematical Systems & Solutions (United States)","ror":"https://ror.org/00apfvn95","country_code":"US","type":"company","lineage":["https://openalex.org/I4210090226"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Lior Pachter","raw_affiliation_strings":["Department of Computing and Mathematical Sciences , Pasadena, CA 91125, USA","Division of Biology and Biological Engineering, California Institute of Technology , Pasadena, CA 91125, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computing and Mathematical Sciences , Pasadena, CA 91125, USA","institution_ids":["https://openalex.org/I4210090226"]},{"raw_affiliation_string":"Division of Biology and Biological Engineering, California Institute of Technology , Pasadena, CA 91125, USA","institution_ids":["https://openalex.org/I122411786"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5029305307","display_name":"A. Sina Booeshaghi","orcid":"https://orcid.org/0000-0002-6442-4502"},"institutions":[{"id":"https://openalex.org/I122411786","display_name":"California Institute of Technology","ror":"https://ror.org/05dxps055","country_code":"US","type":"education","lineage":["https://openalex.org/I122411786"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"A Sina Booeshaghi","raw_affiliation_strings":["Department of Mechanical Engineering, California Institute of Technology , Pasadena, CA 91125, USA"],"affiliations":[{"raw_affiliation_string":"Department of Mechanical Engineering, California Institute of Technology , Pasadena, CA 91125, USA","institution_ids":["https://openalex.org/I122411786"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5020008219","https://openalex.org/A5029305307"],"corresponding_institution_ids":["https://openalex.org/I122411786","https://openalex.org/I4210090226"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.604,"has_fulltext":true,"cited_by_count":31,"citation_normalized_percentile":{"value":0.90961439,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"39","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.993399977684021,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9711999893188477,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/metadata","display_name":"Metadata","score":0.8790797591209412},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7161294221878052},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.6119720339775085},{"id":"https://openalex.org/keywords/json","display_name":"JSON","score":0.5631299614906311},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4786157011985779},{"id":"https://openalex.org/keywords/leverage","display_name":"Leverage (statistics)","score":0.4518900513648987},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4431047737598419},{"id":"https://openalex.org/keywords/raw-data","display_name":"Raw data","score":0.42672210931777954},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.35465216636657715},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.07045924663543701}],"concepts":[{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.8790797591209412},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7161294221878052},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.6119720339775085},{"id":"https://openalex.org/C2780416260","wikidata":"https://www.wikidata.org/wiki/Q2063","display_name":"JSON","level":2,"score":0.5631299614906311},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4786157011985779},{"id":"https://openalex.org/C153083717","wikidata":"https://www.wikidata.org/wiki/Q6535263","display_name":"Leverage (statistics)","level":2,"score":0.4518900513648987},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4431047737598419},{"id":"https://openalex.org/C132964779","wikidata":"https://www.wikidata.org/wiki/Q2110223","display_name":"Raw data","level":2,"score":0.42672210931777954},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.35465216636657715},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.07045924663543701},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000071253","descriptor_name":"Metadata","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000071253","descriptor_name":"Metadata","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000071253","descriptor_name":"Metadata","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btac667","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac667","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac667/48942763/btac667.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36610997","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36610997","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:9883619","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9883619","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC9883619/pdf/btac667.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btac667","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac667","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac667/48942763/btac667.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3497591915","display_name":null,"funder_award_id":"(NIH)","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4667119938","display_name":null,"funder_award_id":"U19MH11483","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4760074400","display_name":null,"funder_award_id":"U19MH114830","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4313702127.pdf","grobid_xml":"https://content.openalex.org/works/W4313702127.grobid-xml"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W2043702114","https://openalex.org/W2135323299","https://openalex.org/W2259938310","https://openalex.org/W2767826728","https://openalex.org/W2795489598","https://openalex.org/W2907094739","https://openalex.org/W2949216109","https://openalex.org/W2949612967","https://openalex.org/W2949631084","https://openalex.org/W2949680846","https://openalex.org/W2951403620","https://openalex.org/W3002281830","https://openalex.org/W3003185440","https://openalex.org/W3028213583","https://openalex.org/W3095215879","https://openalex.org/W3107487008","https://openalex.org/W3109640704","https://openalex.org/W3145635506","https://openalex.org/W3156677136","https://openalex.org/W3159409148","https://openalex.org/W3194665116","https://openalex.org/W3200726150","https://openalex.org/W3211014030","https://openalex.org/W4236345772","https://openalex.org/W4313702077","https://openalex.org/W6749953947","https://openalex.org/W6785109090"],"related_works":["https://openalex.org/W2753132265","https://openalex.org/W4234766820","https://openalex.org/W4321232174","https://openalex.org/W3117520771","https://openalex.org/W2482048793","https://openalex.org/W4388027365","https://openalex.org/W3113257914","https://openalex.org/W2938860153","https://openalex.org/W4312551432","https://openalex.org/W4238373172"],"abstract_inverted_index":{"ffq":[0],"is":[1],"free":[2],"and":[3,6],"open":[4],"source,":[5],"the":[7],"code":[8],"can":[9],"be":[10],"found":[11],"here:":[12],"https://github.com/pachterlab/ffq.":[13]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":13},{"year":2022,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2023-01-08T00:00:00"}
